Background Hepatitis B virus (HBV) gene and protein variations are frequently been seen in chronic patients. The aims of study were to determine the genotypes as well as the patterns of variations distribution in chronically-infected patients from the central part of Iran. Methods: The surface gene was amplified, sequenced and subsequently aligned using international and national Iranian database. Results: All strains belonged to genotype D, subgenotype D1 and subtype ayw2. Of all 62 mutations occurred at 39 nucleotide positions, 31 (50%) were missense (amino acid altering) and 31 (50%) were silent (no amino acid changing). At the amino acid level, 30 substitutions occurred, however, 3 were in positions 122 and 127, corresponded to subtypic determination. 22 (73%) out of 30 amino acid mutations occurred in different immune epitopes within surface protein, of which 12 (54.54%) in B cell epitopes in 10 residues; 5 (45.45%) in T helper epitopes in positions; 5 (22.73%) in inside CTL epitopes in 4 residues. Conclusion: The distribution of amino acid mutations as well as the ratio between silent and missense nucleotide mutations showed a narrowly focused immune pressure had already been on the surface protein in these patients, led to the emergence of escape mutants in these patients.